Sequence
atgc intronic sequence ATGC exonic sequence...gggaatagattctagtgatatagtgtaatggtcctctacatacgaagctcgtgtaaatctttgatcaaaatcttatctttgtgttttgggtttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 1
gggaatagattcta-gtgatatagtgtaatggtcctctacatacgaagctcgtgtaaatctttgatcaaaatc--ttatctttgtgttttgggtttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG
| ||||| ||| | | | ||| | | ||| | ||| | || | || | | ||| || | || | ||||||||||| |||||| | ||||||| |||||||| ||||| || || |||||||| || || || ||||||||||
---ctttttttctaagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
upper sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G26250.2 (Glycine max), 3'ss of exon 1
gggaatagattctagtgatatagtgtaatggtcctctacatacgaagctcgtgtaaatctttgatcaaaatc--ttatctttgtgttttgggtttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG
|||| | | | ||| | | ||| | ||| | || | || | | ||| || | || | ||||||||||| |||||| | ||||||| |||||||| ||||| || || |||||||| || || || ||||||||||
-----------taagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagaaagttcagAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
upper sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 1
-gggaatagattctagtgatata-gtgtaatggtcctctacatacgaagctcgtgtaaatctttgatcaaaatcttatctttgtgttttgggtttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG
| | | |||| | | | |||| || | | || | ||||| || | || | | | | | | ||| || ||| | ||||||||| |||||||| |||||||||||||||| ||||| ||||| |||||||| || || || || ||||| ||||
tgaaatttgattttgtatgtgtgcgtgtcctgatttcatgtatg-gtttagtgtgtatatatgtggatatatgtatttatgtatgtattattttt-tctcagAAAGTGCAAAAGGCGCTGTTGCAATCAGATGTCCAATCTAAATCAGATAAAAGCCCTGTCACAGTGGCTGACTATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|19874586|gb|AU235417.1|AU235417EST: AGCTTGATGCTGCTAAGAAAGCTGCTTCACTCGCTGCTCGTCTCTGTCAG AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAA
genomic: AGCTTGATGCTGCTAAGAAAGCTGCTTCACTCGCTGCTCGTCTCTGTCAGgttagggttt ... tttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAA
EST:
gi|116482884|gb|EG525476.1|EG525476EST: AGCTTGATGCTGCTAAGAAAGCTGCTTCACTCGCTGCTCGTCTCTGTCAG AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAA
genomic: AGCTTGATGCTGCTAAGAAAGCTGCTTCACTCGCTGCTCGTCTCTGTCAGgttagggttt ... tttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctcgtgtaaatctttgatcaaaatcttatctttgtgttttgggtttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG
ctttgat putative branch site (score: 5)
tttgtttc putative PPT
aaaatcttatcttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggaatagattctagtgatatagtgtaatggtcctctacatacgaagctcgtgtaaatctttgatcaaaatcttatctttgtgttttgggtttgtttcagAAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - -ctacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttttgg